


Chuck VS the Secret War

by vandevere



Series: An Alien Verse [4]
Category: Chuck (TV), The X-Files
Genre: AU, Gen, Multiple Crossovers
Language: English
Status: In-Progress
Published: 2019-06-01
Updated: 2019-06-08
Packaged: 2020-04-06 04:19:45
Rating: Teen And Up Audiences
Warnings: Creator Chose Not To Use Archive Warnings
Chapters: 5
Words: 4,175
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/19055113
Author URL: https://archiveofourown.org/users/vandevere/pseuds/vandevere
Summary: Sequel to Chuck VS the Alien Colonists, Prequel to A Mercenary's Tale.  Operation Bartowski gets a new NSA Handler who's a mite more than he seems at first glance.  References additional Crossover materiel not covered in the other Fanfics





	1. Chapter 1

Chuck vs the Secret War

_**Note: This story references multiple TV shows and movies. Try to guess who the OC is…** _

_Prologue_

_NYC, 2002_

_Colonel Diane Beckman steps into the bar, looking for the man she's been hunting for these last ten years._

_The bartender is busy wiping the table, cleaning up everything, ready to close up the shop. It's the wee hours of the night, almost closing time, and most of the patrons have departed, gone home for the night, save for one lonely soul, asleep, head down on the table._

_**Ah…** _ _Beckman regards the bartender._ _**He's the one…** _

_He's a big man, broad across chest and shoulders, six-four or five, craggy features, with a full head of silver-white hair._

" _It's almost closin' time," There's more than a hint of Texas in his rough-sounding voice. "I can sell you one drink, but that's all."_

" _I'm not thirsty," Beckman steps up to the bar counter, takes a photograph out, and slides it across the counter, to the man._

_He stops wiping the table to look at it. Then, the damp cloth slips from seemingly nerveless fingers…_

_It's one of those old-timey black and white photographs from the Nineteenth Century. Three men…a United States Marshall, and two of his deputies._

_The man touches the photo gingerly, index finger resting on one of the deputies, an exact duplicate of the man himself._

_He looks up._

" _How the hell did you find me?" he rasps._

_Beckman sighs. This will take some explaining._

" _We need you," she takes a seat at the counter. "You erased a threat to Earth in the Fifties…"_

" _Totally by accident," the man grunts sourly. "Wrong place…right time. Hang on a sec…"_

_He steps out from behind the counter, walks over to the sleeping customer. Beckman barely hears the muffled conversation between the two, as her target gently hustles the other man out of the bar, then closes, and locks the door._

" _Now, we're alone," he addresses Beckman. "What do you want of me?"_

…..

_2010_

_Castle_

Sarah Walker was feeling somber. John Casey had died three months ago, killed by an alien virus.

The  _NSA_  hadn't sent in a replacement yet. Walker was fairly sure that, mourning notwithstanding, a replacement for John Casey would be coming soon.

Beckman had announced that she would be arriving at Castle just before Lunch.

_Will Casey's replacement be with her?_

Walker was disposed to dislike the replacement, whoever he turned out to be.

_He-whoever he is-won't be John Casey…_

… _.._

Everyone was assembled at Castle, waiting on General Diane Beckman, and the new  _NSA_ Handler...

"Wonder what he's like?" Chuck mused.

He didn't have to wonder long. The door leading to the secret basement entry opened, and two people stepped inside.

Chuck had long since stopped thinking of Beckman as a potential enemy. He had seen her grieve over John Casey's death, had even held her as she wept.

Diane Beckman was a friend, someone both he and Sarah could trust.

Years ago, Chuck had been thrust into this dangerous world of spies. He was the Intersect, the man with all the world's secrets, and a whole bushel basket full of talents and abilities, implanted into his brain.

He hadn't wanted it, hadn't wanted the danger, the killing, that went with it.

Now, due to the trust he had in General Beckman, he willingly entered into this world, with all the danger, and pure insanity that was part of it.

The dangers they all faced now were not limited to the purely terrestrial.

_We're fighting a Secret War…_

That was Operation Bartowski's main responsibility now. Other agents could fight against the Russians, the Chinese, and the Homegrown threats.

_**Our** _ _war is against the Colonists. To make sure John's death isn't in vain…_

Bartowski knew, trusted, and loved, General Diane Beckman. She was family now.

So, he turned his attention to the man who accompanied her, and was promptly inundated by a Flash…

_Dain Hacker…Born Eighteen Twenty-Five in Abilene, Texas, to Selma Hacker, biological Father unknown…Deputy to US Marshall Matthew Dillon from Eighteen Seventy to Eighteen Ninety…Instrumental in the foiling of an Alien Colonist Incursion in Road Prison, Gainesville, Florida, in Nineteen Fifty-five…_

…..

Sarah Walker knew the look of a Flash when she saw one. So, keeping a watchful eye on the newcomer, she waited for the revelation, whatever it turned out to be…

" _Eighteen Twenty-five?"_ Chuck squeaked. "For real?"

Dain Hacker was a big man; around John Casey's size, with craggy features, hazel-gray eyes, and silver hair. He snorted at Chuck's exclamation.

"She told me you had ways of known' things," he nodded at General Beckman. "I'd rather that didn't get out."

"Yeah…" Chuck said. "But how are you our  _NSA_ replacement? You're not even  _in_  the  _NSA…_ "

"Mr. Hacker has talents that are most apt for Operation Bartowski's  _Primary Mission,_ " General Beckman said. "As I'm sure you will recognize from your Flash…"

"That what you call what he does?" Hacker spoke up. "Flashin'?"

"Yeah…" Chuck nodded. "Wow…We're all weird in one way or another, I guess. What do we call you?"

…..

"Call me Dain," Hacker looked at the kid; about as likeable as a puppy. He'd read the dossier on the boy, of course, once he had been tapped to replace John Casey.

It wasn't just Bartowski's ability to use the Intersect, and it wasn't just the sheer amount of cases solved by Operation Bartowski.

_The kid has a working brain and knows how to use it…_

"I take it Mr. Hacker meets with your approval?" General Beckman spoke dryly.

"Yeah…" the boy stood, held out a hand. "Welcome to Operation Bartowski..."


	2. Chapter 2

**Summary for the Chapter:**

> Dain Hacker accidentally repeats history

_2017_

Operation Bartowski was perhaps the strangest gig Dain Hacker had ever been assigned to; with his job as a prison guard at Road Prison Work Camp in Florida, in the  _Fifties,_  coming in a  _very_ close second.

The reason wasn't all that far to seek.

_Aliens in both places…_

Of course, by now the Aliens were literally everywhere.

_Wonder what Matt would think if he knew what lay ahead for Earth one hundred-plus years after his time…_

Of note over the next few years was the Bartowski wedding, followed a few years later by the birth of twins; a boy and a girl.

Apparently, there wasn't as much actual field work as there used to be. Instead, Chuck would mosey down to Castle, and sort through thousands of photos scanned by multiple different operatives over the last twenty-four hours. Occasionally, the kid would Flash on those photos, and a team would be sent out to deal with it…whatever it was.

As General Diane Beckman put it, Chuck Bartowski was too valuable an asset to be casually risked in the open field.

Also, much to everyone's surprise, Bartowski was developing into a first-rate strategist and tactician.

Of course, that didn't necessarily mean Operation Bartowski was entirely free from danger. Sometimes, the Team did have to go out and see to things personally. And, sometimes, things went pear-shaped.

Such as right now…

…..

"I thought they said it was safe!" Dain Hacker could hear Chuck grousing over his ear-wig.

_Both of us…stuck on the outer wall of a high rise during high afternoon…_

Agents of the Ring were here, and Hacker hoped they weren't in the high rise across the street.

_Stuck here, like a pair of dumb flies on a wall. It'd be a duck shoot._

Hacker looked up, looking for an open window, a balcony or porch…

_Anything…_

He, at least, had a utility belt securing him to the wall.

Chuck didn't.

If the kid lost his grip, it would be a thirty-story drop.

_Oh, Mother Dear, pray what is that which looks like strawberry jam?_

_Hush hush, my dear, 'tis your Papa, run over by a tram._

There were days Dain Hacker wished he'd never heard that bit of doggerel.

"Uh-oh…" he heard Chuck's panicked whisper, looked up.

_Kid's losing his grip…_

Hacker saw the open window off to the right.

Just in time…

Chuck fell, and time stopped.

Hacker, somehow, managed to grab the kid, arm or leg, it didn't really matter, and hurled Bartowski in the general direction of the open window, praying as hard as he could…

The kid flew in through the window, like a scored basket, and Hacker sighed in relief. The boy wasn't going to die a strawberry-colored smear on the sidewalk.

Now, Hacker crept over to that open window, hoping Ring Agents wouldn't decide to try plinking away at him.

He could hear gunfire, thankfully not from the window he had just chu… _tossed…_ Chuck in through.

_Walker's keeping the Ring busy…_

Then, he climbed in through the window, and now, he and Chuck were out of the line of fire. It was a very nicely appointed living room, with a huge plasma TV mounted on the wall.

Hacker remembered how stunned he had been when radio first started. Then came the telephone, and TV, and now everyone was connected, literally connected, all over the world.

He recollected himself.

_First order of business, see how Chuck Bartowski is…_

Bartowski seemed to be fine. But Hacker could see tears in the kid's eyes.

"Boy?"

…..

"Boy?" the worry in Hacker's voice was clear.

"I'm okay, Dain," Chuck wiped the tears away.

_You just_ _**had** _ _to do that, didn't you? You just had to catch me when I fell…_

Of course, if he hadn't Chuck would be very dead right now.

But Chuck would never forget how, only a few short years before, John Casey had done the  _exact_  same thing.

_You! I love you!_

_Keep it in your pants Bartowski!_

"You all right, boy?" Hacker's Texas-accented voice brought him back to now.

"Yeah…" Chuck gave himself a shake, reached into his pocket, pulled out the thing that had brought them here, to this particular mission.

A USB Drive carrying proof that the Ring had, indeed, been infiltrated by the Alien Colonists.

_Just as Diane had feared…_

The NSA, at least, was clear. Mandatory genetic testing of all Federal employees had cleared the NSA of any dangerous elements. There had been a few surprises along the way.

FBI Agents Dana Katherine Scully,  _and_ Fox William Mulder were both found to have Alien DNA.

But not the Immortal who was squatting by his side. Not Dain Hacker.

Hacker's immortality was simply the result of a  _de novo_ mutation.

_Just nature's way of hurling a cream pie in everyone's faces…_

Chuck felt Hacker place a comforting hand on his shoulder.

"Let's get out of here," the older man rumbled.


	3. Chapter 3

_Somewhere in Florida, 1953_

_**You'd think I'd have learned by now not to be careless…** _

_Dain Hacker muttered a few choice obscenities under his breath as he drove his old car, as fast as the twisty old road permitted._

_He'd bumped into an old friend from the Great War, what the kids nowadays called World War I to differentiate it from the even greater war that followed in the Forties._

" _ **Dain! You old sod! You haven't aged a day! C'mon and have a drink with me, and we'll talk about the old days!"**_

_That would have been fine and all. But apparently, there were a few people-mostly secret government types-who seemed to be aware that there was an Immortal running around, hiding under various and sundry names._

_Right now, Hacker was using the alias, Andrew Dillon. He was fairly sure Matt wouldn't have minded._

_Anyway, these secret agent types were after him; for what, he couldn't fathom._

_**Unless they're after the reason I don't seem to age…** _

_That put a chill in his blood. What might greedy men do to get immortality for themselves?_

_So, there he was, in an old car, speeding down this twisty old Florida road._

_Hacker didn't see the other car, coming in the opposite direction, until it was too late._

_One too wide turn, and both cars went off the road, tumbling end over end, coming to rest side-by-side…_

…..

_2017_

_Castle_

"I can't believe it!" Sarah Walker grumbled. "They want us to investigate  _dog training companies?"_

"Yep," Chuck Bartowski shared his wife's perturbation.

_Dogs? As trained assassins?_

But,  _someone_ … _somewhere_ …was training dogs to kill specifically targeted individuals.

The list of suspects was long, and included the Ring, the Syndicate, or whatever was left of it, and even the Alien Colonists.

"Just look at this batch we've got now," Dain Hacker sounded slightly honked off about it too. "The quicker we get this done, the quicker it'll be done and over with…"

The man took a seat, black and bitter coffee in hand. Chuck sighed, sat down, and got to it…

Shuffling through phots and ads, waiting for Dear Old Intersect to fire…

He was sort of startled when it actually  _did._

A personally owned and operated company, small, with only a few employees, and a spectacular reputation among its clientele…

As usual, Bartowski felt the Intersect flare behind his eyes, and info-photos and script-downloaded directly into his brain…

"Huh…" Chuck sat back. "Dain…This guy once worked at the same place as you. In that Florida Prison work camp."

He handed the photo to Hacker.

"I'll be damned…" Dain Hacker looked down at the photo in his hands. "We all used to call him,  _Dog Boy_. Those dogs would do  _anything_ for him. Even run themselves to death…"

"You think he would allow his dogs to be used as assassins?" Walker asked.

"Not the guy I knew," Hacker gave the photo back to Chuck. " _He_ took it hard when one of his dogs had a hard time, and  _especially_ when one of them died. The dogs loved him because  _he_ loved them; like they were his own children. He would never have allowed anyone to train  _his_  dogs to be killers."

"But he worked at the same prison camp as you back then," Sarah Walker pointed out.

"Yeah, Walker," Hacker sighed.

"One of these days, Dain, you're gonna have to tell us how you wound up working at a prison work camp."

Hacker bowed his head in response to Chuck.

"Later," he said.

…..

_Florida 1953_

_Dain Hacker opened his eyes groggily, head throbbing._

_**The other car…** _

_It lay, about five feet away, the driver slumped over the steering wheel._

_Staggering out, Hacker made his way, reeling a little, over to the other car. The driver side window had shattered under the impact._

_Hacker reached in, checked for a pulse._

_Nothing…_

_The steering wheel was wet._

_**Blood…he's dead…** _

_Hacker pulled the driver back to get a look at the other man's face. Got the shock of his life._

_The dead man was a complete doppelgänger. Same exact size, same exact face, same exact silver-gray hair._

_**Dead as the proverbial door nail…** _

_The man was dead, though, and Hacker was fairly sure those operatives, whoever they were, were getting close._

_It took a few minutes to carry the body to his totaled car, to switch wallets, and steal items from the other man's car._

_In the nick of time too…_

_Four cars…_ _**Four** _ _of them…coming up together, agents,_ _**armed** _ _agents, getting out, guns all drawn._

_On him._

" _He hit my car," Hacker gestured back at the dead man's now-empty car. "I was just checking on him when you guys arrived."_

" _Out of my way…" the agent in charge shoved Hacker to the side, bent in to check the body slumped at the wheel._

" _Damn…he's dead…" The agent swung around. "How did this happen?"_

_Hacker shrugged, put as much bewilderment into his voice as he could._

" _His car just barreled right into mine."_

" _ID," the agent snapped, hand out._

_Sighing, Hacker took out the dead man's wallet. The man snatched it right out of his hands, opened it, and riffled though the contents._

" _Junior Warden Thomas M. Godfrey…" the man read the name off the ID card._

_**At least I now know who I'm pretending to be…** _

" _Your car looks to be totaled," the man handed the wallet back. "We can call for a tow…"_

" _Yeah…thanks."_

_Suddenly, Dain Hacker's legs were shaking. He was going to escape them this time._

_**Next time, I might not be so lucky…** _


	4. Chapter 4

**Summary for the Chapter:**

> Xover with Paul Newman Movie "Cool Hand Luke"

"It's the Schaeffer Obedience School," Sarah Walker read off the sheet. "Owned and operated by Anthony Schaeffer."

"Yeah. That was his name, though we hardly ever used it. Are you really going to tell him the truth?" Dain Hacker parked the minivan directly across the street from the building.

"He's seen an alien incursion before, Dain," Chuck Bartowski reminded him. "You were there too."

"Yeah…" Hacker sighed. "I was. I'll be here, if you need me."

"All right," Smiling, Walker turned to her husband as Dain Hacker brought out today's paper.

"Ready, Chuck?"

"Yes," Chuck Bartowski stepped out of the minivan, held the door for his wife. "Let's do this."

Inside, the offices were comfortable, neither too hot, nor too cool, the walls decorated with photos of dogs and their proud owners.

"Mr. and Mrs. Bartowski?" the receptionist had apparently been told to expect them. "Mr. Schaeffer will see you now."

…..

Chuck Bartowski's first sight of Anthony Schaeffer was as the older man finished up his current training session; the pup in question an exuberant juvenile Black and Tan Coon Hound getting it's first experience of Leash Training.

Schaeffer was pushing eighty now, full head of gray hair, slightly stooped. But Bartowski could feel the patience, and love from the man as he trained the puppy. Five minutes later, the young couple arrived to take their puppy home, Schaeffer explaining how to leash and house train their puppy…

"Be gentle, firm, and  _regular_ ," Schaeffer explained in his soft-spoken, southern-accented voice. "Nothing disrupts training like irregularity. Your little guy will need to be leash-walked at least twice every day."

"We'll do that…" the husband took the leash, and the couple left, guiding the puppy to the parking lot.

That done, Schaeffer motioned his new visitors to join him in his office.

"I was told you had information some of my dogs were being misused."

"Some of the dogs you train for commercial use." Walker replied.

"Which companies, and  _how_  are they being misused?"

"Please read this file," Walker took a folder out of her purse, handed it to Schaeffer. "It seems these particular entities have been using your dogs to kill people."

Not all of those… _entities_ …were terrestrial in origin.

Schaeffer paled upon hearing that, opened the folder, read the contents. After a while, he put the folder down.

"Shit…" he muttered. "It's… _them_  again…isn't it?"

"You've  _seen_  them, haven't you?" Chuck leaned forward.

"Yeah…" Schaeffer nodded. "Right up close and personal, and none of the rest of us would've known if not for Tom Godfrey. Funny thing, though…He disappeared right after, and left the rest of us with the mess. Dead alien bodies and missing prisoners. Most of  _them_  fled when Godfrey unmasked the Boss. Not that I blame them. I wanted to run myself, but who would look after my dogs? Damndest thing. They bleed  _green_ , you know…"

He sighed.

"Wonder what happened to Godfrey, though," he added. "Just after he disappeared, all these suits-federal Agents, I think, came in. They weren't interested in green-blooded aliens. Not even a little bit. They wanted  _Godfrey_. For what I couldn't tell. But the man was  _gone_. Like the wind."

"Come with us, Mr. Schaeffer," Chuck said. "Let us help you protect your dogs."

…..

_Castle_

It had been an unexpectedly emotional reunion for Dain Hacker. He hadn't liked the job of Prison Work Camp Warden, hadn't liked the possibility of having to shoot inmates when they tried to run. Fortunately, that hadn't happened.

Hacker, hiding under the alias of Junior Warden Thomas M. Godfrey, had learned something very important working there, at Road Prison in Florida. That a glowering silence, enhanced by reflective shades, and a near total lack of emotional reaction translated into one  _very_ scary dude, as one of the inmates put it…

Now, all these years later, sitting over coffee with Anthony Schaeffer… _Dog Boy_ …He felt almost at the point of tears, couldn't rightly say why…

Schaeffer had immediately recognized him.

_Damn…what's it been…sixty years? My god, Tom! You haven't aged a day!_

Even now, all these years later, with NSA doctors studying him, he still didn't know why he didn't age.

_Born in Eighteen-twenty-five, worked as a Deputy for Matt Dillon in the Eighteen Seventies, worked as a Prison Warden in Florida in the Nineteen Fifties. Now, I'm sort of a Secret Agent. They've scanned me, read my DNA…_

_Nobody has a clue why I don't age…_


	5. Chapter 5

_Castle_

Dain Hacker watched as the NSA doctor drew blood from his right arm. Thankfully, needles didn't make him go wobbly.

Unlike some folk, including grown men, he had known over the years...

"How long before you know if it will work, Doc?" he asked.

"We're fairly sure it will work this time," the doctor said. "Even if only in a semi-permanent way…"

They had finally found the answer to Hacker's immortality. Problem was it was highly idiosyncratic. Generally, inserting Hacker's DNA into another individual's genetic code resulted in no result at all, leaving the test subjects no better, or worse off than before. Still, that was  _way_ better than what happened when one inserted the DNA of a Human/Alien Hybrid into someone else.

The end result of  _that_  was usually a quick, and  _very_  nasty death.

_And the ones who don't die wind up mutating, going full alien, and joining the other side…_

Dain Hacker's DNA, with its imperfect penetration, was the NSA's best hope-its only hope, really-of creating people capable of making truly long-range plans. Thing was, as an anti-aging device, it was an imperfect tool.

The medical scientists had managed, however, to synthesize it. So, as imperfect as it was, at least they were able to mass-produce it.

_Pills…_

You could theoretically live forever, as long as you took a pill every day.

But,  _why_ , after so many years of hiding, under countless aliases,was Dain Hacker co-operating with the NSA? Dain Hacker had fought so hard, and so long, to avoid co-operating with all the other agencies, the CIA, the FBI, and the DoD. The answer was simple.

John Casey…

…..

Chuck Bartowski had taken Dain Hacker on a very important trip. They had flown, by helicopter, to this secluded glade, one of the few known sources of Magnetite Ore. For Bartowski, the place, shady, warm, with soft green grass, was a shrine.

John Casey had died here, was now interred in the featureless wall of gray Magnetite.

"Look…" Chuck Bartowski had instructed, fingers pointing out the signs of drilling.

_Drilling…_

_Sonofabitch…_ Dain Hacker felt a thrill of fear shiver its way down his spine.

_They drilled for John Casey…drilled for his DNA…_

In his own way, John Casey was an even more unique genetic specimen than Dain Hacker could ever be.

_A true Human/Alien Hybrid, and also a candidate for what the NSA called the Alien Colonists' Super Soldier Program. The genes within him would make a powerful weapon. In the wrong hands, a world-ending weapon…_

The NSA, under General Diane Beckman's firm guidance, had found many planets capable of supporting life. Now, their scientists were busy making, and testing, starships.

Not rockets.

_Starships…_

Starships capable of transporting colonists to other planetary systems.

Now, the NSA's task was to fight the aliens to a standstill, keep them at bay until humanity could make a mass escape to the stars.

_Away from the conquering aliens…_

Hacker stared at the wall of Magnetite Ore, at the clear marks of drilling.

"Was Diane able to find out who did the drilling?" he asked Bartowski.

"Not the Aliens," Chuck said. "Thank God…"

"Then…whom?"

The kid sighed at Hacker's question.

"We think it's an organization with the ultimate aim of taking Earth back. A few geneticists have been associated with this group. We  _think_  they might be capable, if not now then certainly later, of genetically designing an individual that's immune to the Alien Virus. Such an individual's blood might even serve as a strong vaccine."

"That kind of genetic research would take time," Hacker pointed out.

"We know," Chuck Bartowski faced him. "They probably won't have time to do this before Crunch Time."

_Crunch Time…The day we have to leave Earth…_

"That why you all need the Immortality?"

"Yeah, Dain…" Chuck sighed again. "So, some of us will still be alive and able to help when John Casey's clone is made."

_Here_  was another reason why Dain Hacker was co-operating with the NSA, why he allowed them to draw his blood and do experiments to attain Immortality.

_Loyalty…_

_Beckman and Chuck don't want Immortality just to live forever. They want it so they can find the as yet unborn clone of a friend. They want Immortality so they can save their friend…_

Surely,  _that_  was reason enough to co-operate with the NSA…


End file.
